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<a href="#pub-methods">Public Member Functions</a> &#124;
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<div class="title">moltk::Aligner::Scorer Class Reference</div>  </div>
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<!-- doxytag: class="moltk::Aligner::Scorer" -->
<p>QueryPosition is an alignment column specialized to efficiently compute an alignment score with a TargetPosition.  
 <a href="classmoltk_1_1Aligner_1_1Scorer.html#details">More...</a></p>

<p><code>#include &lt;<a class="el" href="Aligner_8hpp_source.html">Aligner.hpp</a>&gt;</code></p>
<div class="dynheader">
Inheritance diagram for moltk::Aligner::Scorer:</div>
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<div class="center"><img src="classmoltk_1_1Aligner_1_1Scorer__inherit__graph.png" border="0" usemap="#moltk_1_1Aligner_1_1Scorer_inherit__map" alt="Inheritance graph"/></div>
<map name="moltk_1_1Aligner_1_1Scorer_inherit__map" id="moltk_1_1Aligner_1_1Scorer_inherit__map">
<area shape="rect" id="node3" href="classmoltk_1_1MatrixScorer.html" title="MatrixScorer scores alignments using a residue type matrix such as BLOSUM62 or PAM250." alt="" coords="11,80,147,107"/></map>
<center><span class="legend">[<a href="graph_legend.html">legend</a>]</span></center></div>
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Collaboration diagram for moltk::Aligner::Scorer:</div>
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<area shape="rect" id="node2" href="structmoltk_1_1units_1_1Quantity.html" title="Quantity represents a physical value with a unit, such as &quot;5.6 nanometers&quot;." alt="" coords="5,96,203,123"/></map>
<center><span class="legend">[<a href="graph_legend.html">legend</a>]</span></center></div>

<p><a href="classmoltk_1_1Aligner_1_1Scorer-members.html">List of all members.</a></p>
<table class="memberdecls">
<tr><td colspan="2"><h2><a name="pub-methods"></a>
Public Member Functions</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner_1_1Scorer.html#acdd1d2e2c6d447444eba9155ff92f07b">Scorer</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual std::vector&lt; const <br class="typebreak"/>
<a class="el" href="classmoltk_1_1Aligner.html#a919e45f4aa79b2df746f81e65c3c122c">QueryPosition</a> * &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner_1_1Scorer.html#a1934ebea834e741cc07f6d863dd5910f">create_query_positions</a> (const <a class="el" href="classmoltk_1_1Alignment.html">Alignment</a> &amp;) const =0</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual std::vector&lt; const <br class="typebreak"/>
<a class="el" href="classmoltk_1_1Aligner.html#aa110c27fb88b954bf18360f50ad23bb1">TargetPosition</a> * &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner_1_1Scorer.html#a420778fb221136afde4ba61b1778c84d">create_target_positions</a> (const <a class="el" href="classmoltk_1_1Alignment.html">Alignment</a> &amp;) const =0</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner_1_1Scorer.html#a3a2423f141a527da14a45f1a19155333">get_end_gaps_free</a> () const </td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner_1_1Scorer.html#aa163edd66b5c82b40a48803b0df20340">set_end_gaps_free</a> (bool f)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="classmoltk_1_1Aligner.html#a22df03b2c1450636a9ab52e28976c2b3">Information</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner_1_1Scorer.html#a566a3d93e556549bbe86c953b9711b90">get_default_gap_open_penalty</a> () const </td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight"><a class="el" href="classmoltk_1_1Alignment.html" title="Alignment represents a set of aligned macromolecule sequences and/or structures.">Alignment</a> score reduction for initiating an alignment gap.  <a href="#a566a3d93e556549bbe86c953b9711b90"></a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner_1_1Scorer.html#ace04554094ed9997395dd2d1ef243651">set_default_gap_open_penalty</a> (<a class="el" href="classmoltk_1_1Aligner.html#a22df03b2c1450636a9ab52e28976c2b3">Information</a> penalty)</td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Set alignment score reduction for initiating an alignment gap.  <a href="#ace04554094ed9997395dd2d1ef243651"></a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="classmoltk_1_1Aligner.html#a22df03b2c1450636a9ab52e28976c2b3">Information</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner_1_1Scorer.html#aab647817b02c7c92073db07b39618766">get_default_gap_extension_penalty</a> () const </td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight"><a class="el" href="classmoltk_1_1Alignment.html" title="Alignment represents a set of aligned macromolecule sequences and/or structures.">Alignment</a> score reduction for increasing the length of an alignment gap by one position.  <a href="#aab647817b02c7c92073db07b39618766"></a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner_1_1Scorer.html#af010e62c8d82ef395c68ce1ae1298310">set_default_gap_extension_penalty</a> (<a class="el" href="classmoltk_1_1Aligner.html#a22df03b2c1450636a9ab52e28976c2b3">Information</a> penalty)</td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Set <a class="el" href="classmoltk_1_1Alignment.html" title="Alignment represents a set of aligned macromolecule sequences and/or structures.">Alignment</a> score reduction for increasing the length of an alignment gap by one position.  <a href="#af010e62c8d82ef395c68ce1ae1298310"></a><br/></td></tr>
<tr><td colspan="2"><h2><a name="pro-attribs"></a>
Protected Attributes</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner_1_1Scorer.html#a6bee0834ae45e55a1e8752ce75852de0">b_end_gaps_free</a></td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="classmoltk_1_1Aligner.html#a22df03b2c1450636a9ab52e28976c2b3">Information</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner_1_1Scorer.html#a7d422e63db39401de4d1f9a006989034">default_gap_open_penalty</a></td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="classmoltk_1_1Aligner.html#a22df03b2c1450636a9ab52e28976c2b3">Information</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner_1_1Scorer.html#a46b73514546c300654ca1d9c1cef7c44">default_gap_extension_penalty</a></td></tr>
</table>
<hr/><a name="details" id="details"></a><h2>Detailed Description</h2>
<div class="textblock"><p>QueryPosition is an alignment column specialized to efficiently compute an alignment score with a TargetPosition. </p>
<p>TargetPosition is an alignment column specialized to efficiently compute an alignment score with a QueryPosition.</p>
<p><a class="el" href="classmoltk_1_1Aligner_1_1Scorer.html" title="QueryPosition is an alignment column specialized to efficiently compute an alignment score with a Tar...">Scorer</a> can convert, in O(m+n) time, dumb sequence and structure residues into TargetPositions and QueryPositions, which can efficiently compute alignment scores. </p>
</div><hr/><h2>Constructor &amp; Destructor Documentation</h2>
<a class="anchor" id="acdd1d2e2c6d447444eba9155ff92f07b"></a><!-- doxytag: member="moltk::Aligner::Scorer::Scorer" ref="acdd1d2e2c6d447444eba9155ff92f07b" args="()" -->
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          <td class="memname">moltk::Aligner::Scorer::Scorer </td>
          <td>(</td>
          <td class="paramname"></td><td>)</td>
          <td><code> [inline]</code></td>
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      </table>
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</div>
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<hr/><h2>Member Function Documentation</h2>
<a class="anchor" id="a1934ebea834e741cc07f6d863dd5910f"></a><!-- doxytag: member="moltk::Aligner::Scorer::create_query_positions" ref="a1934ebea834e741cc07f6d863dd5910f" args="(const Alignment &amp;) const =0" -->
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          <td class="memname">virtual std::vector&lt;const <a class="el" href="classmoltk_1_1Aligner.html#a919e45f4aa79b2df746f81e65c3c122c">QueryPosition</a>*&gt; moltk::Aligner::Scorer::create_query_positions </td>
          <td>(</td>
          <td class="paramtype">const <a class="el" href="classmoltk_1_1Alignment.html">Alignment</a> &amp;&#160;</td>
          <td class="paramname"></td><td>)</td>
          <td> const<code> [pure virtual]</code></td>
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<p>Implemented in <a class="el" href="classmoltk_1_1MatrixScorer.html#ab2fce5a533eabca4a3cbffce57ea1c57">moltk::MatrixScorer</a>.</p>

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<a class="anchor" id="a420778fb221136afde4ba61b1778c84d"></a><!-- doxytag: member="moltk::Aligner::Scorer::create_target_positions" ref="a420778fb221136afde4ba61b1778c84d" args="(const Alignment &amp;) const =0" -->
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          <td class="memname">virtual std::vector&lt;const <a class="el" href="classmoltk_1_1Aligner.html#aa110c27fb88b954bf18360f50ad23bb1">TargetPosition</a>*&gt; moltk::Aligner::Scorer::create_target_positions </td>
          <td>(</td>
          <td class="paramtype">const <a class="el" href="classmoltk_1_1Alignment.html">Alignment</a> &amp;&#160;</td>
          <td class="paramname"></td><td>)</td>
          <td> const<code> [pure virtual]</code></td>
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<p>Implemented in <a class="el" href="classmoltk_1_1MatrixScorer.html#aff31e3364e2f75ff92be06ef8483886a">moltk::MatrixScorer</a>.</p>

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<a class="anchor" id="aab647817b02c7c92073db07b39618766"></a><!-- doxytag: member="moltk::Aligner::Scorer::get_default_gap_extension_penalty" ref="aab647817b02c7c92073db07b39618766" args="() const " -->
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          <td class="memname"><a class="el" href="classmoltk_1_1Aligner.html#a22df03b2c1450636a9ab52e28976c2b3">Information</a> moltk::Aligner::Scorer::get_default_gap_extension_penalty </td>
          <td>(</td>
          <td class="paramname"></td><td>)</td>
          <td> const<code> [inline]</code></td>
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<p><a class="el" href="classmoltk_1_1Alignment.html" title="Alignment represents a set of aligned macromolecule sequences and/or structures.">Alignment</a> score reduction for increasing the length of an alignment gap by one position. </p>

</div>
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<a class="anchor" id="a566a3d93e556549bbe86c953b9711b90"></a><!-- doxytag: member="moltk::Aligner::Scorer::get_default_gap_open_penalty" ref="a566a3d93e556549bbe86c953b9711b90" args="() const " -->
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          <td class="memname"><a class="el" href="classmoltk_1_1Aligner.html#a22df03b2c1450636a9ab52e28976c2b3">Information</a> moltk::Aligner::Scorer::get_default_gap_open_penalty </td>
          <td>(</td>
          <td class="paramname"></td><td>)</td>
          <td> const<code> [inline]</code></td>
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<p><a class="el" href="classmoltk_1_1Alignment.html" title="Alignment represents a set of aligned macromolecule sequences and/or structures.">Alignment</a> score reduction for initiating an alignment gap. </p>

</div>
</div>
<a class="anchor" id="a3a2423f141a527da14a45f1a19155333"></a><!-- doxytag: member="moltk::Aligner::Scorer::get_end_gaps_free" ref="a3a2423f141a527da14a45f1a19155333" args="() const " -->
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          <td class="memname">bool moltk::Aligner::Scorer::get_end_gaps_free </td>
          <td>(</td>
          <td class="paramname"></td><td>)</td>
          <td> const<code> [inline]</code></td>
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<a class="anchor" id="af010e62c8d82ef395c68ce1ae1298310"></a><!-- doxytag: member="moltk::Aligner::Scorer::set_default_gap_extension_penalty" ref="af010e62c8d82ef395c68ce1ae1298310" args="(Information penalty)" -->
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          <td class="memname">void moltk::Aligner::Scorer::set_default_gap_extension_penalty </td>
          <td>(</td>
          <td class="paramtype"><a class="el" href="classmoltk_1_1Aligner.html#a22df03b2c1450636a9ab52e28976c2b3">Information</a>&#160;</td>
          <td class="paramname"><em>penalty</em></td><td>)</td>
          <td><code> [inline]</code></td>
        </tr>
      </table>
</div>
<div class="memdoc">

<p>Set <a class="el" href="classmoltk_1_1Alignment.html" title="Alignment represents a set of aligned macromolecule sequences and/or structures.">Alignment</a> score reduction for increasing the length of an alignment gap by one position. </p>

</div>
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<a class="anchor" id="ace04554094ed9997395dd2d1ef243651"></a><!-- doxytag: member="moltk::Aligner::Scorer::set_default_gap_open_penalty" ref="ace04554094ed9997395dd2d1ef243651" args="(Information penalty)" -->
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          <td class="memname">void moltk::Aligner::Scorer::set_default_gap_open_penalty </td>
          <td>(</td>
          <td class="paramtype"><a class="el" href="classmoltk_1_1Aligner.html#a22df03b2c1450636a9ab52e28976c2b3">Information</a>&#160;</td>
          <td class="paramname"><em>penalty</em></td><td>)</td>
          <td><code> [inline]</code></td>
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<p>Set alignment score reduction for initiating an alignment gap. </p>

</div>
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<a class="anchor" id="aa163edd66b5c82b40a48803b0df20340"></a><!-- doxytag: member="moltk::Aligner::Scorer::set_end_gaps_free" ref="aa163edd66b5c82b40a48803b0df20340" args="(bool f)" -->
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          <td class="memname">void moltk::Aligner::Scorer::set_end_gaps_free </td>
          <td>(</td>
          <td class="paramtype">bool&#160;</td>
          <td class="paramname"><em>f</em></td><td>)</td>
          <td><code> [inline]</code></td>
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<hr/><h2>Member Data Documentation</h2>
<a class="anchor" id="a6bee0834ae45e55a1e8752ce75852de0"></a><!-- doxytag: member="moltk::Aligner::Scorer::b_end_gaps_free" ref="a6bee0834ae45e55a1e8752ce75852de0" args="" -->
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          <td class="memname">bool <a class="el" href="classmoltk_1_1Aligner_1_1Scorer.html#a6bee0834ae45e55a1e8752ce75852de0">moltk::Aligner::Scorer::b_end_gaps_free</a><code> [protected]</code></td>
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<a class="anchor" id="a46b73514546c300654ca1d9c1cef7c44"></a><!-- doxytag: member="moltk::Aligner::Scorer::default_gap_extension_penalty" ref="a46b73514546c300654ca1d9c1cef7c44" args="" -->
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          <td class="memname"><a class="el" href="classmoltk_1_1Aligner.html#a22df03b2c1450636a9ab52e28976c2b3">Information</a> <a class="el" href="classmoltk_1_1Aligner_1_1Scorer.html#a46b73514546c300654ca1d9c1cef7c44">moltk::Aligner::Scorer::default_gap_extension_penalty</a><code> [protected]</code></td>
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<a class="anchor" id="a7d422e63db39401de4d1f9a006989034"></a><!-- doxytag: member="moltk::Aligner::Scorer::default_gap_open_penalty" ref="a7d422e63db39401de4d1f9a006989034" args="" -->
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          <td class="memname"><a class="el" href="classmoltk_1_1Aligner.html#a22df03b2c1450636a9ab52e28976c2b3">Information</a> <a class="el" href="classmoltk_1_1Aligner_1_1Scorer.html#a7d422e63db39401de4d1f9a006989034">moltk::Aligner::Scorer::default_gap_open_penalty</a><code> [protected]</code></td>
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<hr/>The documentation for this class was generated from the following file:<ul>
<li>moltk/<a class="el" href="Aligner_8hpp_source.html">Aligner.hpp</a></li>
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